You can re-run it. Send the recon-all.log if you still have problems.
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Dong, Yilei
Sent: Thursday, March 21, 2024 1:26 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct: Command not found error
External Email - Use Caution
Hi Yujing,
My recon-all just ended at that point. It didn't make it through the entire
processing stream. Should I rerun the entire process or make any additional
adjustments when I submit my script again?
Sincerely,
Yilei
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, March 21, 2024 6:11 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] nu_correct: Command not found error
It looks like Freesurfer can't find minc toolkit binaries on your system.
Did your recon-all finish fine? I think FS 7.2 recon-all is configured to use
ANTS N4BiasFieldCorrection for nu correct by default.
This is from your log:
"mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1
--proto-iters 1000 --distance 50"
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Dong, Yilei
Sent: Wednesday, March 20, 2024 2:01 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] nu_correct: Command not found error
External Email - Use Caution
Hi Freesurfer support,
Recently, I submitted a script to run recon-all on 100 mri images on UCSD's
computing cluster, called EXPANSE. I get an error file that says "nu_correct:
Command not found. FREESURFER: Undefined variable." The sample error file and
the output file I have attached for one of the subjects are
recon-all-slurm.29376886.exp-5-44.err & recon-all-slurm.29376886.exp-5-44.out
respectively. The script I used to submit the job via slurm is called
recon-all-slurm.sb.
I googled the error and found that someone else who had a similar situation did
not source their Freesurfer environment correctly. Would this be the same thing
for us as well? The main thing for us is Freesurfer/7.2.0 already has been
available as a module for us on EXPANSE.
Sincerely,
Yilei
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